Method for removing genetic linkage in a plant

ABSTRACT

The current disclosure relates to the field of plants, in particular to the fields of plant breeding and plant genetics. More particular, the disclosure concerns inventive methodology that may be useful in improving plant properties. In particular the invention may be useful in removing linkage drag. Also provided are plant and plant parts obtained with the method disclosed herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/655,633 filed Jun. 25, 2015, which is the National Stage ofInternational Application No. PCT/NL2013/050939 filed on Dec. 20, 2013,which was published on Jul. 3, 2014, as WO 2014/104878 A1, and whichclaims the benefit of U.S. Application No. 61/746,399 filed Dec. 27,2012, the entire disclosures of which are incorporated herein byreference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-WEB and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Jun. 23, 2017, isnamed 085342-0601SequenceListing.txt and is 2.33 KB.

FIELD OF THE INVENTION

The current disclosure relates to the field of plants, in particular tothe fields of plant breeding and plant genetics. More particular, thedisclosure concerns inventive methodology that may be useful inimproving plant properties.

PRIOR ART

Recombination results in the new arrangement of genes by variousmechanisms such as assortment and segregation, crossing over, geneconversion and transformation. Recombination in plants can occur atnumerous stages in plant development. There are two main differentclasses of recombination in plant cells, homologous recombination (HR)and non-homologous end joining (NHEJ). The HR recombination pathwayinvolves rearrangements between DNA molecules that share the same DNAsequence, whether this is on the same or different chromosomes. This isin contrast with the NHEJ pathway, that is able to generaterearrangements between any DNA molecules, irrespective of any DNAhomology between them. The HR pathway is thought to be active in all thedifferent types of plant cell, For instance, HR plays an essential rolein gamete formation by promoting crossovers between sister chromatidsfor correct chromosome segregation and the recombination of differentparental alleles (meiotic HR). The HR pathway is also active in mitoticcells where it is mainly involved in the repair of DNA damage at a locususing the sequence information present on the homologous undamaged locus(mitotic HR). This can be present on the same or different chromosome asthe damaged locus. The NHEJ pathway is also active in both meiotic andmitotic cells and is very effective at joining non-homologous DNA endstogether. One of the main differences between the HR and NHEJ pathwaysis the fidelity of the process. While HR between related DNA sequencesresults in recombination in which the DNA sequence of bothmolecules/loci is preserved the NHEJ pathway often generates smallmutations at the position where the recombination occurs, which initself can be mutagenic.

Plant breeding involves the selection of optimal parental plants whichare then crossed and progeny from this cross with improved growthcharacteristics are selected. Plant breeding has been very successfulover the last 100 years in domesticating a wide range of plant speciesand improving significantly the yield and quality of plant products.

This has been achieved through the selection of allelic variation thatprovides improvements in both plant cultivation and consumption traits.Typically, a cross is performed between two parent plants to produce thehybrid F1 progeny which are then selfed to create homozygous alleles andthe resulting F2 progeny are screened for the phenotype of interest.When plants are crossed to form the hybrid (F1), recombination(crossovers) occur between the different homologous parental plantchromosomes during meiosis, shuffling the genetic informationcontributed by each parent.

Recombination during meiosis (meiotic HR) is a (semi-) random, homologydependent, process producing male and female gametes that each carrydifferent sets of alleles from the parental plants. If a particularcombination of parental loci in the progeny is desired then manyindividuals must be screened to select those that have inherited thedesired parental alleles. Screening can be performed based solely on thephenotype, or as is more often the case, by using molecular markerstightly linked to the allele(s) of interest. This marker assistedbreeding (MAB) approach has the advantage that the plants of a F2population can be screened at an early growth stage so that largepopulations of mature plants do not need to be maintained and also theycan be screened for the presence of many markers linked to multiplealleles. Therefore it is clear that the process of meiotic recombinationis the main driver in plant breeding and that processes that affect thiscan lead to bottlenecks in the breeding process.

The total world population is expected to increase significantly in thecoming decades and there is a realization that the yield of many cropsmust also increase while at the same time utilizing the same area ofarable land and using fewer resources such as water and fertilizer.Plant breeding has a large part to play in improving crop yield throughthe introduction of novel alleles present in the germplasm. However,conventional plant breeding has led to a reduction in the total amountof allelic variation present in cultivated crops, either throughconscious selection against traits that were viewed to be deleterious orthrough unconscious loss of alleles due to the lack of selectionpressure on variation that was considered neutral at the time. Due tothe reduced allelic variation in cultivated species, the novel allelesthat can confer such traits such as novel biotic and abiotic resistancesare unlikely to be present in the cultivated germplasm. One likelysource of such alleles is in unadapted wild germplasm. Wild germplasmhas been extensively used to improve the germplasm of cultivated specieswhen either the growing conditions or the consumer preferences changeand the existing gene pool does not have the necessary genetic variationto meet the changing needs. The success of using wild germplasm dependson several factors such as the breadth of variation that can be accessedthrough crossing (e.g. plant incompatibility, species barriers), thespeed at which novel genetic variation can be transferred to address thequickly changing needs and finally how much variation can be transferredfrom a wild species without the transfer of severe negative effects(linkage drag). Linkage drag may be described as the presence of geneticlinkage between two loci, for example one desirable and the otherundesirable, on the same chromosome. As a consequence of this geneticlinkage the two loci are inherited together during normal meiosis.Unfortunately, with the methods available in the art, removing thegenetic linkage between such desired and undesired genes in a plant, andobtaining a plant with only the desired genes and associated traits, hasturned out to be difficult, time consuming, and in various casesimpossible.

Meiosis is responsible for the formation of reduced gametes (egg cellsor pollen) containing half the genetic complement of the parent plant.During meiosis, meiotic recombination occurs between the parentalchromosomes resulting in a mixing of parental alleles so that thegametes carry different combinations of parental loci producingdifferent patterns of genetic variation in the progeny plants. Meioticrecombination usually occurs between the euchromatic regions of theparental chromosomes where there is a high degree of synteny, at boththe structural and the DNA level. It is well known in the literaturethat recombination (crossovers) between parental chromosomes isinhibited in regions which are structurally different (such as largedeletions, insertions or inversions) or lack DNA sequence identity. Thisis less of a problem when the parents are derived from a common lineageand are therefore genetically similar but becomes a larger problem whenconsidering crosses with wild germplasm which are likely to begenetically more diverse than the cultivated lines. In such cases theregions at which crossovers can occur between the chromosomes of thewild germplasm and the cultivated germplasm is and inhibited by theaforementioned structural differences in the DNA. When performing across between plant lines with cultivated and wild germplasm, F2 plantsare selected carrying the desired alleles and then these are backcrossedmultiples times with the cultivated plant line, while continuing toselect for plants carrying the desired wild germplasm allele(s), toincrease the percentage of the genome contributed by the cultivatedparent while decreasing the percentage of the genome from the wildparent. In an ideal situation this will result in a plant with thegenome of the cultivated parent but carrying a small locus(introgression) from the wild germplasm. As stated before, thisbackcrossing process is completely dependent on normal meioticrecombination occurring between loci from the two parents. However, dueto the presence of structural and sequence differences between theparents meiotic recombination can be suppressed, leading to the presenceof large introgressions from the wild germplasm that cannot be madesmaller (Canady et al. (2006) Genetics 174, 1775-1788).

As meiotic recombination is suppressed at such regions, subsequentbackcrosses are not successful in decreasing the introgression size.This can be a particular problem when both the desired positive traitand also a negative trait are located on the introgression as thesecannot be easily separated using meiotic recombination. This explainswhy there is often linkage drag that cannot be easily broken onintrogressions derived from wild germplasm. The approach usually takento break such linkage drag is to screen many more plants than normal fora recombination event between the two loci. This is sometimes possible,but can be very expensive and has no guarantee of success as the degreeof recombination suppression is unknown. There are many examples ofintrogressions at which no further recombination occurs despite seriousefforts to screen very large plant populations. Several publications(e.g. WO03/104451 and WO00/54574) have described methods for enhancingMHR in plants which may increase the chance of obtaining the rarerecombination events in regions of suppressed meiotic recombination suchas in regions with linkage drag. However, the methods described in thesepublications propose treatments that enhance the HR pathway between allthe homologous loci in the cell which is undesirable in breedingmaterial. In addition, these treatments are also often inherentlymutagenic which alter the DNA sequence genome wide and lead tounpredictable phenotypes. For example, the publication EP0270120 teachesthat linkage drag can be broken by the growth of plant cells in tissueculture on medium containing high levels of a mutagenic plant growthregulator. As with the other publications the recombination rate genomewide will be affected and thus the plants generated by this method wouldbe unsuitable for further breeding.

Therefore there is a clear need in the art for reproducible and easiermethodology allowing the manipulation of the genome of plants, inparticular in breeding processes, and in particular allowing thebreaking/removing of genetic linkage between two loci on the samechromosome, in particular wherein such loci are both localized in a partof the chromosome were recombination is suppressed.

PROBLEMS SOLVED BY THE PRESENT INVENTION

We surprisingly found that the above identified need in the prior artmay be solved by using the NHEJ pathway to induce a recombination eventspecifically only at the introgression with the linkage drag andavoiding altering the recombination or mutation rates throughout therest of the genome. Indeed, in this invention we disclose a novel use ofthe NHEJ pathway in plant breeding, specifically for breaking linkagedrag. Here we disclose a method which can be applied in somatic plantcells and allows creating a translocation by NHEJ at any specificposition between homologous or homeologous chromosomes, for example in aF1 hybrid. The methodology may be used for a wide range of breedingapplications, for example for the purpose of elimination of linkagedrag, for the purpose of targeted manipulation of polyploid genomes, forthe purpose of the production of custom introgressions, for the purposeof simplified fine mapping and for the purpose of generation of genefusions.

In more detail, the invention involves the introduction of double strandbreaks, for example using site specific nucleases (including nucleasesystems), into plant cells, including plant protoplasts. The sitespecific nucleases may be targeted to specific identical sequences atthe corresponding position on both homologous chromosomes. These theninduce a DNA double strand break on each chromosome which withunexpected high frequency (in approx. 0.8% of cells) are re-joinedresulting in an exchange of chromosome arms, which leads to an inducedtargeted translocation. One additional important advantage of thismethod is that it only requires tissue culture facilities to identifythe desired recombination events rather than screening large plantpopulations to identify random meiotic HR events, all of which requiresa greenhouse. Therefore, use of the method for the purposes given abovemay also lead to a large cost reduction in the breeding processesitself.

The method according to the invention may, for example, be used for thepurpose of:

-   -   a. Breaking linkage drag: Resistance to severe viruses such as        TMV and TYCLV have been introduced from wild tomato species and        the genes conferring resistance are present on large        introgression fragments which are recombinationally silent.        There are also genes on these introgressions that negatively        affect yield (linkage drag) but cannot be recombined away from        the source of resistance. However, this yield loss is accepted        as the virus resistance is so valuable. The technique described        herein can be used for the purpose of breaking up the        introgression fragment at defined positions, thus generating        lines with the virus resistance but lacking the linkage drag.        All forms of linkage drag are a large problem in breeding and        will continue to slow down and complicate plant breeding in the        future.    -   b. Tailored introgressions: Any chromosomal region of known        sequence can be linked to any other sequence on the homologous        chromosome. This allows one to define the size of the        introgression that one would want to have in a final product. In        fact, the introgression could comprise a single gene.    -   c. Fine mapping: Gene mapping uses meiotic recombination to link        genes to markers, but is not effective when meiotic        recombination is suppressed or when many genes are closely        linked. The method disclosed herein, leading to translocation,        can be used to divide an introgression fragment into smaller        regions which can then be genotyped using markers or be        phenotyped. In this way one can quickly identify causal genes.    -   d. Intra-genic recombination: New sources of resistance are        needed as new biotypes of pathogens evolve. Resistance genes are        normally present in clusters and recombination between these        generates new genes that confer new resistances. However, these        are low frequency events and difficult to find. Translocations        can be used to combine parts (domains) of resistance genes        present in clusters on different chromosomes to create new        combinations of domains conferring novel resistances.    -   e. Homozygosity in polyploidy species: Several polyploidy plant        species are allopolyploids, meaning that the separate genomes do        not recombine during meiosis. This can be problematic when one        of the genomes carries a negative phenotype at a chromosomal        position because this cannot be eliminated. Translocations can        be induced between the genomes and through selfing a situation        can be created whereby whole chromosome arms become completely        homozygous. This can also be used to transfer mutations induced        in the chromosomes of one genome to the chromosomes of the other        genome, which is particularly useful if such mutations are        recessive (which is nearly always the case).

With the realization of the inventive thought to apply the methoddisclosed herein for the various purposes disclosed above, the skilledperson will be able to indeed apply these method for the above givenpurposes.

SUMMARY OF THE INVENTION

In one aspect there is provided for a method for removing geneticlinkage between a first locus A and a second locus B present on a firstplant chromosome in a plant or plant cell, wherein (meiotic)recombination between, and including, the location of said first locus Aand the location of said second locus B on the chromosome is suppressed.The method comprises the steps of providing at least one plant cellcomprising said first chromosome comprising said first locus A and saidsecond locus B and further comprising at least a second chromosome,wherein said chromosomes are homologous or homeologous chromosomes ofeach other; introducing a double strand break in the first chromosome,wherein the double strand break in the first chromosome is introducedbetween said first locus A and said second locus B thereby providing afirst part of the first chromosome comprising the first locus A and asecond part of the first chromosome comprising the second locus B andintroducing a double strand break in the second chromosome, therebyproviding a first part of the second chromosome and a second part of thesecond chromosome. The double strand break in the first chromosomeand/or the double strand break in the second chromosome is introduced byat least one site-specific nuclease, preferably selected from the groupconsisting of zinc finger nuclease, meganuclease, TAL-effector nucleaseand the Cas9/crRNA/tracrRNA CRISPR system.

Optionally, but in certain embodiment preferred, the method furthercomprises identifying using the at least one plant cell obtained atleast one plant cell wherein the genetic linkage between the first locusA and the second locus B on the first chromosome has been removed, andfurther, wherein the first part of the first chromosome comprising thefirst locus A is ligated to the second part of the second chromosome.

The double strand break in the first chromosome and/or the double strandbreak in the second chromosome is/are introduced by at least onesite-specific nuclease, preferably selected from the group consisting ofzinc finger nuclease, meganuclease, TAL-effector nuclease (TALENS) andthe Cas9/crRNA/tracrRNA CRISPR system.

In a particularly preferred embodiment the method is performed whereinthe first chromosome comprises said first locus A and said second locusB, wherein said first locus A is linked to a desirable trait of a firstcharacter and said second locus B is linked to a undesirable trait ofsaid first character or a second character; and wherein said secondchromosome does not comprise a locus that is identical to said secondlocus B linked to a undesirable trait of said first character or asecond character, and; one double strand break is introduced betweensaid first locus A and said second locus B on the first chromosome andat a corresponding locus or location in the second chromosome. Thisembodiment allows for the removal of linkage drag between desired andundesired traits commonly seen in (hybrid) plants.

Accordingly, there is also provided for a method for providing a plantP1 obtained from a plant P2, wherein said plant P2 is characterized bythe presence of genetic linkage between a first locus A and a secondlocus B on a first chromosome, wherein (meiotic) recombination between,and including, the location of said first locus A and the location ofsaid second locus B on the chromosome is suppressed, and wherein saidplant P1 is characterized by the absence of said genetic linkage, themethod comprising providing at least one plant cell comprising saidfirst chromosome comprising said first locus A and said second locus Band further comprising at least a second chromosome, wherein saidchromosomes are homologous or homeologous chromosomes of each other;introducing a double strand break in the first chromosome, wherein thedouble strand break in the first chromosome is introduced between saidfirst locus A and said second locus B thereby providing a first part ofthe first chromosome comprising the first locus A and a second part ofthe first chromosome comprising the second locus B and introducing adouble strand break in the second chromosome, thereby providing a firstpart of the second chromosome and a second part of the secondchromosome, and; optionally, identifying from the at least one plantcell obtained at least one plant cell wherein the genetic linkagebetween the first locus A and the second locus B on the first chromosomehas been removed, and further, wherein the first part of the firstchromosome comprising the first locus A is ligated to the second part ofthe second chromosome. Plant P1 can thus be regenerated.

According to another aspect of the invention there is provided for theuse of a site-specific nuclease, preferably selected from the groupconsisting of a zinc finger nuclease, a meganuclease, a TAL-effectornuclease and the Cas9/crRNA/tracrRNA CRISPR system for removing geneticlinkage between a first locus A and a second locus B present on a firstchromosome, wherein (meiotic) recombination between, and including, thelocation of said first locus A and the location of said second locus Bon the chromosome is suppressed.

According to a final aspect of the invention there is provided for aplant, plant part, fruit or seed obtainable by or obtained by the methodaccording to the invention, or the use according to the invention.

DESCRIPTION OF THE DRAWINGS

FIG. 1: Left panel: Two homologous chromosomes are indicated inside asingle protoplast with the light grey section on one chromosomerepresenting an introgression (light grey) from an unadapted wildspecies at which meiotic recombination does not occur (recombinationsuppression). The boxes in the introgression represent the locus givingthe positive phenotype (black) and the locus giving the negativephenotype. The plasmid expressing the double-strand break-inducingenzyme is shown as a circle. The arrows represent the positions in thechromosome at which a DNA DSB is induced by the site-specific nuclease.Middle panel: DNA DSB is induced in both homologous chromosomes. Rightpanel: DSB repair leading to a reciprocal translocation. The positiveand negative loci are no longer linked.

FIG. 2 provides the sequence of Solanum pennellii ALS2 locus. The ALS2open reading frame is underlined. The target sequence for the ZFN isshown in bold italics.

FIG. 2a shows the results of testing of primers specifically amplifyingeither the Solanum pennellii ALS2 locus (left panel) or the WT ALS2locus (right panel). L, ladder; BC, F1 line derived from a IL7-3×M82cross; M82, WT tomato line; IL7-3, line containing S. pennelliiintrogression on chromosome VII; B, water control.

FIG. 3 shows small deletions induced in protoplasts of the IL7-3 and M82lines. Upper line, sequence of the target site. The ZFN binding sitesare underlined. The small deletions that were found in M82 and IL7-3protoplasts are shown. The dashes represent missing nucleotides.

FIG. 4: M82 ALS2 and S. pennellii ALS2 sequences are shown (top) withthe ZFN binding site underlined and the single nucleotide polymorphisms(SNP) between the loci shown in bold lowercase. The ZFN binding sitesare underlined. The first SNP between the loci after the ZFN bindingsite is 449 bps downstream as is indicated. The primers used for all thePCR amplification were 11_13680 (S. pennellii ALS2 forward primer) and12_07231 (M82 ALS2 reverse primer). M82 & IL7-3, sequence of cloned PCRproducts derived from transfection of protoplasts from the parentallines with pKG7402. F1, sequence of cloned PCR products derived fromtransfection of protoplasts from the F1 line with a pKG7381 (35S::GFP).F1×ZFN, sequence of cloned PCR products derived from transfection ofprotoplasts of the F1 line with pKG7402. The presence of small INDEL'sat ZFN binding site is represented by missing nucleotides. Clones #1 and#2 were isolated using primers 12_11216+12_11217 in a non-selective PCRreaction.

FIG. 5 schematically shows targeted translocations in Brassica napus. 1,the A (dark grey) and C (light grey) genomes are indicated. The locus tobe made homozygous is indicated by a circle. A site-specific nuclease isexpressed in the cell and induced a DSB in all 4 chromosomes at theposition of the dotted line. 2, a targeted translocation occurs betweenthe A and C genomes. 3, after selfing the translocation region and thelocus of interest is homozygous. 4, part of the chromosome arm from theC genome becomes homozygous.

DESCRIPTION Definitions

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The practice of conventionaltechniques in molecular biology, biochemistry, computationalbiochemistry, cell culture, recombinant DNA, bioinformatics, genomics,sequencing and related fields are well-known to those of skill in theart and are discussed, for example, in the following literaturereferences: Sambrook et al., Molecular Cloning. A Laboratory Manual, 2ndEdition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1989; Ausubel et al., Current Protocols in Molecular Biology, John Wiley& Sons, New York, 1987 and periodic updates; and the series Methods inEnzymology, Academic Press, San Diego. For purposes of the presentinvention, the following terms are defined below.

As used herein, the singular forms “a,” “an” and “the” include pluralreferents unless the context clearly dictates otherwise. For example, areference to “a” DNA molecule may include a plurality of the same DNAmolecules (e.g. 10's, 100's, 1000's, 10's of thousands, 100's ofthousands, millions, or more molecules).

The term “and/or” indicates indicate that one or more of the statedcases may occur. In other words, a stated case may either occur alone orin combination with at least one of the stated cases, up to with all ofthe stated cases. The term and/or discloses each stated case alone, aswell as the specific combination of a stated case with at least one ofthe other stated cases, up to with all of the stated cases.

In this disclosure, “comprises,” “comprising,” “containing” and “having”and the like can have the meaning ascribed to them in patent law and canmean “includes,” “including,” and the like; “consisting essentially of”or “consists essentially” likewise has the meaning ascribed in patentlaw and the term is open-ended, allowing for the presence of more thanthat which is recited so long as basic or novel characteristics of thatwhich is recited is not changed by the presence of more than that whichis recited, but excludes prior art embodiments.

As used herein, the term “allele(s)” means any of one or morealternative forms of a gene at a particular locus. In a diploid cell ofan organism, alleles of a given gene are located at a specific location,or locus (loci plural) on a chromosome. One allele is present on eachchromosome of the pair of homologous chromosomes. A diploid or plantspecies may comprise a large number of different alleles at a particularlocus.

A “character” relates to a phenotypical quality of an organism. Acharacter can manifest itself in different traits. For example, theplant can be a plant, having flower colour as a character, and the redor white flowers being the traits A and B of the character. Within thecurrent invention, the character (or trait) can be any, as long asmembers of the organism having a first trait of the character can bephenotypically distinguished from members of the organism having asecond trait of the character. This is not limited to only differencesthat can be directly observed by inspection of an organism, but alsoincludes characters/traits that can become apparent upon furtheranalysis of the organism, for example upon analysis of the resistance tocertain circumstances, or upon analysis of the presence of particularmetabolites in such organism.

“Genetic linkage” between loci on the same chromosome is understood bythe skilled person to refer to those loci that are located relative toeach other on the same chromosome such that they are normally inheritedtogether during meiosis. For example, genes whose loci are nearer toeach other are less likely to be separated onto different chromatidsduring chromosomal crossover, and are therefore said to be geneticallylinked. Another example is when loci are both located in the samesegment of the chromosome characterized by “Suppression of (meiotic)recombination” (see below). Also in this case, the loci are likely to beinherited together during meiosis.

As used herein, the term “heterozygous” means a genetic conditionexisting when two different alleles reside at a specific locus.Conversely, as used herein, the term “homozygous” means a geneticcondition existing when two identical alleles reside at a specificlocus, but are positioned individually on corresponding pairs ofhomologous chromosomes in the cell.

The term “homeologous” or “homoeologous” chromosome, is used to describethe relationship of similar chromosomes brought together followinginter-species hybridization and allopolyploidization, and whoserelationship was completely homologous in an ancestral species. Twochromosomes are said to be homeologous when they are derived from twodifferent genomes, but share characteristics such as similar nucleotidesequences, similar gene order synteny and are placed in correspondingpositions in the karyograms of both genomes.

The term “homologous” chromosome is used to describe the relationship ofsimilar chromosomes that pair at meiosis. Two chromosomes are homologousto each other when they are capable of forming chromosome pairs inmeiosis through a synaptonemal complex.

The enzymatic reaction catalysed by a ligase enzyme in which twodouble-stranded DNA molecules are covalently joined together is referredto as ligation. The DNA molecule is said to be “ligated” by thisreaction.

As used herein, the term “locus” (loci plural) means a specific place orplaces or a site on a chromosome where a gene or genetic marker islocated.

The “genotype” is the genetic makeup of a cell, an organism, or anindividual (i.e. the specific allele makeup of the individual) usuallywith reference to a specific character or trait under consideration.

A “phenotype” is the observable characteristics or traits of an organismsuch as its morphology, development, biochemical or physiologicalproperties, phenology, behaviour, and products of behaviour. Phenotypesresult from the expression of the genes of an as well as the influenceof environmental factors and the interactions between the two.

The current disclosure is applicable to a wide range of plants, bothmonocots and dicots. Non-limiting examples include the Cucurbitaceae,Solanaceae and Gramineae, maize/corn (Zea species), wheat (Triticumspecies), barley (e.g. Hordeum vulgare), oat (e.g. Avena sativa),sorghum (Sorghum bicolor), rye (Secale cereale), soybean (Glycine spp,e.g. G. max), cotton (Gossypium species, e.g. G. hirsutum, G.barbadense), Brassica spp. (e.g. B. napus, B. juncea, B. oleracea, B.rapa, etc), sunflower (Helianthus annus), safflower, yam, cassava,alfalfa (Medicago sativa), rice (Oryza species, e.g. O. sativa indicacultivar-group or japonica cultivar-group), forage grasses, pearl millet(Pennisetum spp. e.g. P. glaucum), tree species (Pinus, poplar, fir,plantain, etc), tea, coffea, oil palm, coconut, vegetable species, suchas pea, zucchini, beans (e.g. Phaseolus species), cucumber, artichoke,asparagus, broccoli, garlic, leek, lettuce, onion, radish, lettuce,turnip, Brussels sprouts, carrot, cauliflower, chicory, celery, spinach,endive, fennel, beet, fleshy fruit bearing plants (grapes, peaches,plums, strawberry, mango, apple, plum, cherry, apricot, banana,blackberry, blueberry, citrus, kiwi, figs, lemon, lime, nectarines,raspberry, watermelon, orange, grapefruit, etc.), ornamental species(e.g. Rose, Petunia, Chrysanthemum, Lily, Gerbera species), herbs (mint,parsley, basil, thyme, etc.), woody trees (e.g. species of Populus,Salix, Quercus, Eucalyptus), fibre species e.g. flax (Linumusitatissimum) and hemp (Cannabis sativa), or model organisms, such asArabidopsis thaliana.

For the purposes of the present invention, the term “recombination” isused to indicate the process by which genetic material between two lociis exchanged.

“Suppression of (meiotic) recombination”: the meiotic recombinationbetween two loci on the same chromosome in a hybrid individual issuppressed when less than one crossover or recombination event occurs in2000 offspring individuals after selfing or backcrossing of the hybridplant.

In biology, “a trait” relates to any phenotypical distinctive characterof an individual member of an organism in comparison to (any) otherindividual member of the same organism. Within the context of thecurrent invention the trait can be inherited, i.e. be passed along tonext generations of the organism by means of the genetic information inthe organism. “Trait of the same character” or “trait of saidcharacter”: anyone of a group of at least two traits that exist (orbecame apparent) for a character. For example, in case of the character“colour of the flower”, phenotypical manifestations might comprise blue,red, white, and so on. In the above example blue, red and white are alldifferent traits of the same character.

Throughout this application, various references are cited in parenthesesto describe more fully the state of the art to which this inventionpertains. Full bibliographic information for each citation is found atthe end of the specification, immediately preceding the claims. Thedisclosure of these references is hereby incorporated by reference intothe present disclosure in their entirety.

DETAILED DESCRIPTION

The current invention provides a new and inventive method for removinggenetic linkage between loci present on a chromosome, making it possibleto no longer rely on classical breeding methodology or classicalmarker-assisted breeding. In particular the methodology disclosed hereinallows for achieving recombination in somatic cells at parts of thechromosome characterized by having suppressed (meiotic) recombination,i.e. parts that, under meiotic conditions are normally inheritedtogether. The method allows, in one aspect, for reciprocal chromosometranslocation (cross-over; exchange) between homologous and/orhomeologous chromosomes in somatic cells in areas or parts of thechromosome that are characterized by having suppressed (meiotic)recombination. This, for example, allows for the first time, toefficiently remove genetic linkage between two loci on the samechromosome and both located in such “suppressed (meiotic) recombination”part of the chromosome. In addition, the method allows for this insomatic cells, is DNA sequence independent and does not depend onmeiosis or mitosis.

More in particular there is provided for a method for removing geneticlinkage between a first locus A and a second locus B present on a firstplant chromosome in a plant or plant cell, and wherein (meiotic)recombination between, and including, the location of said first locus Aand the location of said second locus B on the chromosome is suppressed,the method comprising the steps of:

-   -   (a) providing at least one plant cell comprising said first        chromosome comprising said first locus A and said second locus B        and further comprising at least a second chromosome, wherein        said chromosomes are homologous or homeologous chromosomes of        each other;    -   (b) introducing a double strand break in the first chromosome,        wherein the double strand break in the first chromosome is        introduced between said first locus A and said second locus B        thereby providing a first part of the first chromosome        comprising the first locus A and a second part of the first        chromosome comprising the second locus B and        -   introducing a double strand break in the second chromosome,            thereby providing a first part of the second chromosome and            a second part of the second chromosome, and;    -   (c) optionally, identifying using the at least one plant cell        obtained under step (b) at least one plant cell wherein the        genetic linkage between the first locus A and the second locus B        on the first chromosome has been removed, and further, wherein        the first part of the first chromosome comprising the first        locus A is ligated to the second part of the second chromosome,        and wherein the double strand break in the first chromosome        and/or the double strand break in the second chromosome is        introduced by at least one site-specific nuclease, preferably        selected from the group consisting of zinc finger nuclease,        meganuclease, TAL-effector nuclease and the Cas9/crRNA/tracrRNA        CRISPR system.

With the method genetic linkage between to loci A and B, present on thesame chromosome is removed. In other words, after the method accordingto the invention the two original loci A and B are less likely to beinherited together during subsequent meiosis and are in fact not presenttogether on the same chromosome. In a preferred embodiment, locus A andlocus B are present on the same chromosome arm

Locus A and locus B on the first chromosome may be a gene, a promoter, agenetic marker or any sequence present on the first chromosome. Thelocus may or may not be mapped as being the locus for a particularbiological trait. In some embodiments, locus A and/or locus B are a geneand/or part of a gene.

The method is preferably performed on a chromosome present in a plantcell, preferably a plant protoplast and preferably in the presence ofthe other naturally occurring components of such plant cell, includingthe complete set of chromosomes of such plant cell.

In a preferred embodiment, the plant cell is a protoplast. Methods forobtaining and maintaining plant protoplasts are readily available to theskilled person. It was found that the most efficient method of inducing(sequence specific) DNA DSB's in plant cells is through the use of plantprotoplasts. Protoplasts are individual plant cells that lack theprimary and secondary cell walls and are generated by incubating plantparts with a fungus-derived enzyme mixture. Any DNA, such as plasmids,can then be introduced into protoplasts by chemical treatments and anygene of interest present on the plasmid whose expression is driven by asuitable plant promoter can be expressed at high levels due to thethousands of plasmid copies that enter each cell. Gene expression ispreferably transient, lasting e.g. 24-36 hours, as the plasmid is unableto replicate and becomes degraded over time. Additionally, integrationof the plasmid in the plant genome is rare. /pct

Individual plant protoplasts can be induced to divide to formundifferentiated cell clumps called calli and these in turn can beinduced to regenerate leaves and shoots which can then be rooted toproduce plants. A protoplast based system is ideal for the production ofDNA DSB's using any of the methods described herein. The site-specificnuclease can be placed on the plasmid, expressed to a high level, andhigh amount of site-specific protein produced that is able to induce therequired DNA DSB. Protoplasts can be isolated in large numbers (millionsper day) and transfected with plasmid DNA en masse, and the calliderived from these transfected protoplasts are derived from a singleprotoplast cell and so do not suffer from chimaerism.

The locus A and the locus B are however characterized in that they arelocalized on said first chromosome in a part, area or segment that ischaracterized in that (meiotic) recombination of that part, area orsegment is suppressed. As described herein, “suppressed meioticrecombination” ” is meant to indicate that meiotic recombination betweenthe two loci on the same chromosome in a hybrid individual is less thanone crossover or recombination event occurring in 2000 offspringindividuals after selfing or backcrossing of the hybrid plant. In apreferred embodiment this is less than one crossover or recombinantevent occurring in 2500, 5000 or 8000 offspring individuals. A personskilled in the art is aware on how to determine this.

In the method, a double strand break is introduced in the firstchromosome, comprising said first locus A and said second locus B. Theposition or locus where such double strand break is introduced isbetween said first locus A and B. By introducing a double strand breakbetween locus A and B, the chromosome is divided in at least two parts,preferably no more than two parts; one part comprising said locus A andone part comprising said locus B. In the context of the currentinvention, when reference is made to a first part or second part of saidchromosome this may indicate either the part that now comprises thecentromere (i.e. that was in the original chromosome towards (andincluding) the centromere), or the part that, by the introduction of thedouble strand break, now is separated from the centromere (i.e. the partthat was further away from the centre of the chromosome, i.e. closer tothe end of the chromosome (arm), relative to the other part that isformed due to the introduction of a double strand break). If, in thecontext of the current invention a first part of the first chromosome isligated to a second part of the second chromosome, this indicates that apart of the first chromosome that is closer to the centromere of thefirst chromosome is ligated to a part of the second chromosome that isfurther away from the centromere of the second chromosome, relative tothe other part that is formed due to the introduction of the doublestrand break in said chromosome(s) or the other way around. In otherwords, in a re-ligated chromosome comprising a first part of a firstchromosome and a second part of a second chromosome, in one embodimentthe first part was closer to the centromere of the first chromosome andthe second part was further away from the centromere of the secondchromosome, relative to the other part of the same chromosome formed bythe introduction of the double strand break.

It was surprisingly found that, when performing the above steps, plantcells may be identified, using molecular techniques, or simply byregenerating a plant from such cells, wherein the genetic linkagebetween said first locus A and said second locus B has been removed, andwherein there has occurred a cross-over (exchange) between the at leasttwo homologous or homeologous chromosomes such that locus A is presentof a first chromosome and locus B is present on said second homologousor homeologous chromosome. Put otherwise, wherein the homologous orhomeologous chromosomes have been re-organized in that an exchange orcross-over occurred between the at least two chromosomes, and whereinthe locus A and locus B, although being located in an area of thechromosome with suppressed (meiotic) recombination have been separated.

Optionally, therefore, at least one cell may be identified, afterperforming the above steps (a) and (b) wherein the genetic linkagebetween the first locus A and the second locus B on the first chromosomehas been removed, and further, wherein the first part of the firstchromosome comprising the first locus A is ligated to the second part ofthe second chromosome. Alternatively, in some embodiments, the obtainedcells after step (b) may be regenerated into plants, and optionallysubsequently selfed, and the plants thus obtained may be used tophenotypically screen for the removal of the genetic linkage betweenlocus A and B, for example in case locus A and locus B are linked toparticular trait(s) that can be observed.

Preferably step (c) of the method above is performed, i.e. is part ofthe method according to the invention. The skilled person is, based onthe disclosure herein, well aware of how to identify such at least onecell. For example, individual protoplasts may first be separatelypropagated, after which a few of the propagated (clonal) protoplasts maybe analysed, for example using standard DNA sequencing, or amplificationor hybridisation techniques for the re-ligation of the two part of thetwo chromosomes, and/or phenotyping the offspring, and/or fluorescentin-situ hybridisation (FISH).

In a preferred embodiment, when performing step (c) above, the methodfurther comprises identification of those cells wherein in addition alsothe second part of the first chromosome is ligated to the first part ofthe second chromosome. Again, as above, the skilled person is well awareon how to perform such identification.

In a particularly preferred embodiment of the methods disclosed hereinthe plant cell selected is such that the second chromosome does notcomprise a locus that is identical to said first locus A and/or does notcomprise a locus that is identical to said second locus B. In otherwords, although the second chromosome may have an allele of the samelocus A and/or B, it must have at least some sequence difference withthe locus/allele present in the first chromosome. For example, the firstchromosome comprises a locus A or B that may be a first allele of acertain gene, and the second chromosome may comprise another allele forthe same gene. Preferably, in such embodiment, the allele on the firstchromosome and the second chromosome are related to a differentphenotype.

In another embodiment of the methods disclosed herein, the distancebetween said first locus A and said second locus B present on said firstplant chromosome is between one base pair and the length of the entirechromosome. As has been disclosed above, the locus A and locus B on thefirst chromosome are both in (a same) area/part/segment of thechromosome that is characterized by suppressed (meiotic) recombination.A particular additional advantage of the current invention is that nowsuch loci can be easily separated, while still providing surviving andnormal plants even if such loci are either very close to each other orfar removed.

In the methods disclosed herein, the double strand break in the firstchromosome and/or the double strand break in the second chromosomeis/are introduced by at least one site-specific nuclease preferablyselected from zinc finger nuclease, meganuclease, TAL-effector nuclease(TALENS) and the Cas9/crRNA/tracrRNA CRISPR system.

Whereas genotoxic agents that introduce DNA breaks and modificationsrandomly throughtout the genome, the (endo)nucleases used in the currentinvention can nowadays be rationally designed to recognize and bind to aspecific DNA sequence at which a DNA DSB is subsequently induced.

For the current invention four technologies/nuclease systems tointroduce the DSB are preferred: (1) meganucleases, (2) zinc fingernucleases (ZFN), and (3) TAL effector nucleases (TALENs) and (4) theCas9/crRNA/tracrRNA CRISPR system.

Meganucleases, including such homing endonulceases as I-Scel, can bemutated to confer an altered DNA sequence affinity (Belfort and Roberts,1997, Nucleic Axids Res. 25: 3379-3388; Chevalier and Stoddard, 2001,Nucleic Acids Res. 29: 3757-3774) and their activity has been reportedin plants (Kirk, 2000, EMBO J. 19, 5562-566). Meganucleases are alsosometimes referred to as LAGLIDADG Homing Endonucleases (LHE's; Stoddardet al (2011) Structure 19:7-15). Meganucleases differ from Zinc FingerNucleases and TALENs (see below) in that they are naturally occurringgene-targeting proteins that form homodimers comprising two identicalsubunits each about 160 to 200 amino acid residues in size. It has beensuggested they may also function as a single peptide of two tandemrepeat monomers joined together by a linker sequence (Stoddard, 2011).Meganucleases generally recognize a target site of about 20 to 30 basepairs. For an overview of meganucleases and methods to assess mutatedmeganucleases for activity and altered target specificities reference ismade to Stoddards et al (2011). In addition, the use of meganucleaseshas, for example, been described in WO2011154159 and EP2522723. Themeganuclease or the pair of meganucleases, as well as all the othernucleases used in the current invention may be introduced in the plantcell and subsequently (transiently) expressed therein, and using methodswell aware to the skilled person. For example from a chimeric gene or apair of chimeric genes, each comprising a plant expressible promoterlinked to a coding region encoding the meganuclease or one of the pairof meganucleases, and further operationally linked to a DNA regioninvolved in transcription termination and polyadenylation functional ina plant cell.

For the purposes of the present invention, the term “zinc fingernuclease” or “ZFN” refers to a chimeric protein molecule comprising atleast one zinc finger DNA binding domain effectively linked to at leastone nuclease capable of cleaving DNA. Cleavage by a ZFN at a targetlocus results in a double stranded break (DSB) at that locus. Zincfinger nucleases consist of two domains, an array of zinc finger domainsand a nuclease domain, usually derived from the IIS-type restrictionenzyme Fokl. These type IIS restriction enzymes, such as Fokl, recognizespecific DNA sequences and cleave several base pairs downstream of therecognition site. Each zinc finger domain can be engineered to recognizea specific 3 bps triplet and by linking together a number of these alonger DNA sequence can be specifically recognized. The Fokl domain mustdimerise before cutting DNA and so two ZFN proteins are designed totarget sequences on the opposite DNA strands separated by a short spacerregion of 5-6 bps. Binding of both of the ZFN proteins to theirrespective target sequence brings both Fokl domains opposite each otheron the DNA helix in the spacer region where a DNA DSBs is then produced.Many studies have shown that ZFN are effective in inducing small INDEL'sat an endogenous target sequence in many different plant species (Curtin(2012) The Plant Genome, 5, 42-50). Custom-made zinc finger nucleasesare commercially available under the name CompoZr from Sigma-Aldrich(http://www.sigmaaldrich.com/life-science/zinc-finger-nuclease-technology.html).The use of zinc finger nucleases in plants has, for example, beendescribed in WO03087341and WO2011052539. The ZFN used for the currentinvention, as well as all the other nucleases used in the currentinvention, may be introduced in the plant cell and subsequently(transiently) expressed therein, and using methods well aware to theskilled person. For example from a chimeric gene or a pair of chimericgenes, each comprising a plant expressible promoter linked to a codingregion encoding the zinc finger nuclease or one of a pair of zinc fingernucleases, and further operationally linked to a DNA region involved intranscription termination and polyadenylation functional in a plantcell. The publication US2012/0196370 teaches that ZFNs can be used tocreate defined deletions in a eukaryotic genome. In this approach ZFNswhose target sites are separated by up to 120 Kbps and introduced intocells together with a linear “donor” molecule which has at either end aregion of sequence homology each of the separated ZFN target sites.After treatment of animal cell lines with these reagents products couldthen be amplified whereby the region between the ZFN target sites hadbeen replaced by the donor molecule, producing an effective deletion ofthe intervening sequence. In this case the mitotic HR pathway is useddue to the regions of sequence homology present at the ends of the donormolecule. The publication suggests that the donor molecule is essentialto first, drive the accuracy of the mitotic HR reaction and second, toincrease the frequency of the mitotic HR reaction. This is thought to benecessary because the frequency of translocations obtained when justusing the ZFNs is too low for practical application. In contrast to whatis taught in the literature, the current inventors found that specifictranslocations between plant chromosomes can be produced when only asingle ZFN pair is used to generate the DSBs. In contrast to thepublication US2012/0196370 our experiments utilize the NHEJ pathway togenerate translocations as we observe at the chromosome fusion pointssmall deletions that are characteristic for this recombination pathway.When a DNA DSB is induced in only one of the plant chromosomes the DNAends are rejoined by the NHEJ pathway resulting in small deletions. Thefrequency of these small deletions (present in 10% of the cells) is madeup of two components, the cutting efficiency of the ZFN pair andefficiency at which the DSB is repaired by the NHEJ pathway. In thiscase a single DSB is induced on one chromosome so that the DNA ends arein close proximity, resulting in the 10% efficiency. However, for atranslocation to occur DSBs must be produced on two chromosomes that arespatially separated in the nucleus and the interaction of these DNA endsis unlikely resulting in a very low frequency of translocationformation. However, we have found that efficiency of translocationformation (0.8%) in plant cells by the NHEJ pathway is unexpectedlyhigh, only 12 fold lower than the repair of adjacent DNA ends, andtherefore allows easy isolation of individual cells that had undergonethis recombination process. In addition, our method in plant cells doesnot require a “donor” molecule as the frequency and accuracy oftranslocation formation using the NHEJ pathway is already high enoughaccording to our invention for practical application. Thus, the methodaccording to the invention does not need to use such linear donormolecule or donor polynucleotide as described in US2012/0196370

TALENs are site specific nucleases derived from TAL effectors producedby Xanthomonas species which cause a variety of different plantdiseases. During the infection of a plant by Xanthomonas species the TALeffector proteins are introduced into the plant cell. TAL effectorsconsist of a number of repeating protein domains, each of which is ableto specifically recognize and bind to one of the 4 DNA nucleotides(A,T,G,C). Different combinations of these domains are present indifferent TAL effectors and each one binds to a unique DNA sequence inthe plant genome, often in plant gene promoters. pathogen Once bound tothe plant DNA the TAL effector influences plant gene expression toenhance the bacterial pathogenicity. The domains specific for eachnucleotide have been identified and arrays of these domains can beproduced which have high binding affinity for any DNA sequence(Christian, 2010, Genetics 186: 757-761; Cermak et al., 2011, NucleicAcids Res 39:e82; Bogdanove and Voytas, 2011, Science 333: 1843-1846;Boch, 2011, Nature Biotechnology 29:135-136). Commercial custom-madeTALENs are available from Cellectis Bioresearch(http://www.cellectis-bioresearch.com/genome-customization/genomic-scissors/talen).These arrays are then fused to the nuclease domain of Fokl to create aTALEN and, similar to ZFN, two TALEN proteins are used to induce a DNADSB in a spacer region at the target sequence. Several papers havedescribed the use of TALEN's to create mutations at the target sequencespecies (Curtin (2012) The Plant Genome, 5, 42-50). The TALENS used forthe current invention, as well as all the other nucleases used in thecurrent invention, may be introduced in the plant cell and subsequently(transiently) expressed therein, and using methods well aware to theskilled person. For example from a chimeric gene or a pair of chimericgenes, each comprising a plant expressible promoter operably linked to acoding region encoding the TALENS nuclease or one of a pair of TALENSnucleases, and further operationally linked to a DNA region involved intranscription termination and polyadenylation functional in a plantcell. The use of TAL-effector (TALENS) has, for example, been describedin WO201107224.

The CRISPR technology (also herein referred to as theCas9/crRNA/tracrRNA CRISPR system.) is derived from bacteria where it isused as a system to defend against invading molecular pathogens such asplasmids and bacteriophages. Specific loci in the bacterial genomeconsist of arrays of short sequences derived from the genomes ofmolecular pathogens which are the result of previous infections. SmallRNA's (crRNAs) are produced from these loci that interact with thetracrRNA and these RNA molecules together then target the Cas9 proteinto the specific complementary sequence in the molecular pathogen'sgenome. The Cas9 protein has nuclease activity and is able to produce aspecific DNA double strand break (DSB) at the target sequence in thepathogen genome which then becomes degraded. Expression of both the Cas9protein (nuclease), tracrRNA and crRNA (the components of the CRISPRsystem) targeting a genomic sequence in the cells of plants and animalscreates targeted DSBs at the genomic target sequence that is oftenmis-repaired by the cellular DNA machinery, resulting in a smallinsertion or deletion (INDEL) (Feng et al. (2013)Cell Res. 1: 4; Li etal. (2013) Nat. Biotech. 31: 689-691; Nekrasov et al. (2013) Nat.Biotech. 31: 691-693; Shan et al. (2013) Nat. Biotech. 31: 686-688). AnINDEL in the coding sequence of a gene or even in an intron often leadsto loss of gene function. For practical purposes, the tracrRNA and crRNAare usually combined into one chimeric guide RNA (sgRNA); thiscombination of RNAs is included in the definition of theCas9/crRNA/tracrRNA CRISPR system.

Site specific nucleases can induce targeted DSBs at a high efficiencyand thus plants containing INDELs in the target sequence can be easilyidentified. Genome engineering through the use of site specificnucleases such as the CRISPR systems has many applications, especiallyin polyploidy species, and is becoming increasingly important for cropimprovement.

Although in principle one or more of the above-discussed nucleases maybe used, alone or in combination, it is preferred that the double strandbreak in the first chromosome and/or the double strand break in thesecond chromosome is introduced by the same site-specific nuclease, thesame zinc finger nuclease, the same meganuclease, the same TAL-effectornuclease, or the same the Cas9/crRNA/tracrRNA nuclease system. In otherwords, it is preferred to target at a sequence in both the first and thesecond chromosome that may targeted by the same nuclease, for examplebecause the target sequence is identical. Recognizing such a target inboth the first chromosome and the second chromosome is within the skillsof the skilled person, and will not be difficult since the first andsecond chromosome are homologous or homeologous chromosomes sharingparts of the chromosome having high levels of identity, e.g. 100%.

It will be clear to the skilled person, and based on the disclosureherein, in a preferred embodiment of the methods disclosed herein nomore than one double strand break is introduced in the first chromosomeand no more than one double strand break is introduced in the secondchromosome.

In another preferred embodiment of the methods according to theinvention

-   -   i. the first chromosome comprises said first locus A and said        second locus B, wherein said first locus A is linked to a        desirable trait of a first character and said second locus B is        linked to a undesirable trait of said first character or a        second character; and    -   ii. wherein said second chromosome does not comprise a locus        that is identical to said second locus B linked to a undesirable        trait of said first character or a second character, and;    -   iii. one double strand break is introduced between said first        locus A and said second locus B on the first chromosome and at a        corresponding locus or location in the second chromosome.

This embodiment of the method according to the invention provides forovercoming linkage drag. The method provides for separating of a locus Athat is linked to a favourable treat from a locus B that is linked to anunfavourable trait. Both locus A and B may be a genetic marker linked tosaid desired (A) or undesired (B) trait or may be (in) the gene that iscausally linked to the desired or undesired trait. The traits associatedor linked with the locus A and B may or may not be of the samecharacter.

As disclosed above, in a particularly preferred embodiment of themethods disclosed herein the plant cell selected is a such that thesecond chromosome does not comprise a locus that is identical to saidfirst locus A and/or does not comprise a locus that is identical to saidsecond locus B. In other words, although the second chromosome may havean allele of the same locus A and/or B, it must have at least somesequence difference with the locus/allele present in the firstchromosome. For example, the first chromosome comprises a locus A or Bthat may be a first allele of a certain gene, and the second chromosomemay comprise another allele for the same gene. In the context of thecurrent embodiment the skilled person understands that the secondchromosome preferably does not provide a locus that is identical to saidundesired locus B at the first chromosome, or comprises a locus B thatis an undesired allelic variant of such undesired locus B. In otherwords, by this method according to the invention the first chromosome ismodified as such that the undesired locus B originally present on thechromosome is removed and replaces by a corresponding part of thechromosome obtained from the second chromosome, and not containing saidlocus B linked to an undesired trait.

Non-limiting examples of undesirable traits may be a trait selected fromthe group consisting of: a trait that negatively influences thedesirable trait of the first character, reduced yield, reducedresistance to disease or pests, reduced growth, reduced size, reducedamount of seeds, reduced resistance against stress, including salt,heat, cold, water and drought stress. However, as will be understood anytrait of a character may be considered undesirable, depending on thepurpose of the breeders or skilled person, alone or relative to thedesired trait associated to the locus A.

In a further embodiment of the method according to the invention, themethod further comprises regenerating a plant from a plant cell obtainedafter step (b) or step (c) and generating seed from said regeneratedplant by selfing or crossing with another plant and growing a plant fromthe obtained seed and optionally, screening said plant obtained forremoval of genetic linkage. As explained above, the skilled person iswell aware how to perform these steps and how to screen for the removalof genetic linkage.

Preferably the provided plant cell is a somatic plant cell, preferably aprotoplast, and/or a plant cell obtained from a hybrid. The plant cellmay be obtained from any suitable plant, for example as specificallydisclosed herein. The plant cell may be derived from, for examplediploid, triploid, tetraploid, pentaploid, hexaploid, octaploid,decaploid, dodecaploid or an amphidiploid plant.

In line of the disclosure herein, and taking into account allpreferences and modifications discussed herein and in possession of theskilled person, there is also provided for a method for providing aplant P1 obtained from a plant P2, wherein said plant P2 ischaracterized by the presence of genetic linkage between a first locus Aand a second locus B on a first chromosome,

wherein (meiotic) recombination between, and including, the location ofsaid first locus A and the location of said second locus B on thechromosome is suppressed, and wherein said plant P1 is characterized bythe absence of said genetic linkage, the method comprising

-   -   (a) providing at least one plant cell comprising said first        chromosome comprising said first locus A and said second locus B        and further comprising at least a second chromosome, wherein        said chromosomes are homologous or homeologous chromosomes of        each other;    -   (b) introducing a double strand break in the first chromosome,        wherein the double strand break in the first chromosome is        introduced between said first locus A and said second locus B        thereby providing a first part of the first chromosome        comprising the first locus A and a second part of the first        chromosome comprising the second locus B and        -   introducing a double strand break in the second chromosome,            thereby providing a first part of the second chromosome and            a second part of the second chromosome, and;    -   (c) optionally, identifying using the at least one plant cell        obtained under step b) at least one plant cell wherein the        genetic linkage between the first locus A and the second locus B        on the first chromosome has been removed, and further, wherein        the first part of the first chromosome comprising the first        locus A is ligated to the second part of the second chromosome,        and wherein the double strand break in the first chromosome        and/or the double strand break in the second chromosome is        introduced by at least one site-specific nuclease, preferably        selected from the group consisting of zinc finger nuclease,        meganuclease, TAL-effector nuclease and the Cas9/crRNA/tracrRNA        CRISPR system.

Again, preferably step (c) is performed.

According to another aspect there is provided for the use of asite-specific nuclease, preferably selected from the group consisting ofa zinc finger nuclease, a meganuclease, a TAL-effector nuclease and theCas9/crRNA/tracrRNA CRISPR system, for removing genetic linkage betweena first locus A and a second locus B present on a first chromosome,wherein (meiotic) recombination between, and including, the location ofsaid first locus A and the location of said second locus B on thechromosome is suppressed. Preferably there is provided for the usewherein said first locus A is linked to a desirable trait of a firstcharacter and said second locus B is linked to an undesirable trait ofsaid first character or a second character.

Also provided is for the use of a site-specific nuclease, preferablyselected from a zinc finger nuclease, a meganuclease, a TAL-effectornuclease and the Cas9/crRNA/tracrRNA CRISPR system for removing linkagedrag.

In a last aspect there is provided for a plant, plant part, fruit orseed obtainable by or obtained by a methods or uses according to theinvention. In a preferred embodiment there is provided for a group of atleast 2 of such plant, plant part, fruit or seed.

In summary, the disclosed invention, in a non-limiting embodiment,involves inducing crossovers between homologous or homeologous parentalchromosomes in somatic plant protoplasts through the use ofsite-specific nucleases that may induce a specific DNA DSB at the samesequence on both chromosomes. This may be achieved by isolating plantprotoplasts and then introducing the site-specific nuclease present on aplasmid into the protoplasts by a chemical treatment. The site-specificnuclease protein is then produced in the protoplast and induces the DNADSB's. It is believed that the NHEJ system may repair these DSB's byligating the free DNA ends from the different chromosomes together,resulting in an exchange of chromosome arms, also known as a reciprocaltranslocation. Site-specific nucleases can be designed to induce DSB'sat any desired sequence, and thus a reciprocal translocation can beinduced at any point along the homologous parental chromosomes. Onelarge advantage over meiotic recombination is that the joining of DNAends using the method according to the invention is sequence independentand therefore using this approach there is no limitation on the regionsthat can be targeted or exchanged. Therefore, this approach is ideal forbreaking linkage drag in; for example, introgressions which, due tosequence differences, do not recombine during meiosis (are suppressed).There are many examples of important traits in commercially importantcrops species, such as viral TMV and TYLCV resistance in tomato, whichare located on large introgression fragments with severe linkage dragwhich has a negative effect on the plant yield. As these resistances arevaluable, the yield losses are accepted but it will be very beneficialto both plant breeders are growers to break such linkage drag to furtherincrease plant yield.

The ability to create plants containing introgressions with a definedsize is also of great use to plant breeders in general. Populations ofplants, each containing a defined introgression from a wild unadaptedplant species can be produced and used for crop improvement and genediscovery. Genes responsible for novel traits can be mapped moreefficiently by splitting up the introgression on which they lie intosmaller parts and repeating this until the position of the gene ofinterest has been defined. As the generation of targeted translocationsis sequence independent, plant introgression libraries can be generatedmore quickly and precisely all the genomic regions can be equallyrepresented. This decreases the need for screening large F2 populationsfor the desired crossovers, meaning that fewer facilities such asgreenhouse space are required. This method can also be applied to thebreeding of allo-polyploid species such as tobacco, rapeseed or wheat.Allo-polyploid plant species are often the result of an ancienthybridization event between two or more diploid plant species wherebythe separate different genomes do not recombine during meiosis. Forinstance, Brassica napus consists of an A and C genome which do not mixduring meiosis. Therefore, a particular chromosomal region on either ofthe genomes cannot be made completely homozygous through selfing.Protoplasts of B. napus can be isolated and transfected with a plasmidconstruct carrying a site-specific nuclease that induces a DSB at thesame position on both the A and C chromosomes. The cell may thengenerate a reciprocal translocation between the A and C genomes whichwould not be possible to achieve through meiotic recombination. Thesubsequent regenerated plants can then be selfed any plants that arefully homozygous for the translocation in both genomes identified.Targeted translocations can also be very useful for the manipulation ofDNA sequences at the gene level. If a specific promoter has beenidentified that is more active in a wild unadapted plant species than inthe cultivated species then targeted translocations can be used totransfer the active promoter into the genome of the cultivated species.This can be achieved by crossing the two species to produce a F1 line,isolating protoplasts from this, and then expressing a site-specificnuclease in these protoplasts that induces a DSB in both homologouschromosomes at a position just before the transcription start of thegene of interest. The resulting targeted translocation will join theupstream sequences, including the active promoter, to the gene ofinterest this altering its pattern and level of transcription.Similarly, site-specific nucleases can be designed to introduce DSB's atintrons of genes present on different homologous chromosomes. A targetedtranslocation between these DSB's will result in the exchange of genedomains between the homologous chromosomes and the formation of chimericgenes containing domains from each chromosome. In this case, the smalldeletions produced by the NHEJ system are located in the intron itselfand so are unlikely to inhibit gene function.

EXAMPLES Example 1 Inducing a Targeted Translocation at Chromosome VIIin Tomato Protoplasts

The experimental setup for generating targeted translocations in tomatocells is shown in FIG. 1. The approach uses a site specific nuclease, inthis example a zinc finger nuclease, which induces a DNA double strandbreak (DSB) at the same or corresponding genomic position on both of thehomologous chromosomes. A translocation between the chromosomes can thenbe formed when these two DSB's are repaired by joining the DNA endstogether from the other chromosome, thus exchanging the chromosome arms.To detect the formation of translocations, PCR primers were designedthat specifically amplify the ZFN cut site on each chromosome. Once atranslocation has been formed these junctions can be specificallyamplified by using different combinations of these forward and reverseprimers. For specific primer design, sequence differences must bepresent flanking the ZFN cut site on each chromosome. This was achievedby using a tomato line carrying an introgression on chromosome VII fromthe wild tomato species Solanum pennellii. This introgression regioncontains the ZFN target site in the S. pennellii ALS2 gene (SpALS2) andalso enough sequence differences with the wild type ALS2 (WT ALS2) tomake specific primer design possible. The experiment was performed bycreating a F1 hybrid heterozygous for the ALS locus by crossing the WTtomato (M82) with the S. pennellii chromosome VII introgression lineIL7-3. Protoplasts were then produced from this F1 hybrid andtransfected with a plasmid construct which expresses the ZFN thatinduces the DSB at both the WT ALS2 and SpALS2 loci. Using our PCRapproach we were able to detect cells in which a reciprocaltranslocation had occurred. Surprisingly, such events were detectable ata relatively high frequency (0.8%) which was unexpected because the DNADSBs were located on different chromosomes. This is the first reportedevidence that site specific nucleases are able to induce reciprocaltranslocations in plant cells and a demonstration that such events occurat a relatively high frequency. We then went on to grow individual plantprotoplasts to callus and genotyped these calli using PCR to identifythose with the desired translocation. Such calli can be regenerated intoplants and would show a loss of linkage between the markers flanking theintrogression fragment. This approach can be used to decrease the sizeof an introgression fragment in somatic plant protoplasts in a homologyindependent manner.

Zinc Finger Nuclease Construct

For our experiments the plasmid pKG7402 was used. This plasmid contains2 zinc finger nuclease genes designed to bind and induce a DNA doublestrand break at the tomato acetolactate synthase (ALS) genes (ALS1 andALS2). ALS1 is located on the short arm of chromosome III and ALS2 islocated on the long arm of chromosome VII.

Plant Material

Solanum lycopersicum line (IL7-3) containing an introgression from thetomato wild species Solanum pennellii on chromosome VII was used. Thisintrogression fragment is approximately 56 cM in size and makes up themajority of the long arm of this chromosome (Eshed, Y & Zamir, D. (1995)Genetics 141: 1147-1162) and includes the ALS2 gene of S. pennellii.Plants homozygous for this introgression fragment were backcrossed tothe parent line (M82) and F1 seeds were collected. These were thensterilized and germinated on synthetic medium (MS20: MS medium+vitamins(Duchefa) 4.4 g/l, sucrose 20 g/l, micro agar 8 g/l) in high jars at16/8 h photoperiod of 2000 lux at 25° C. and 60-70% RH. The parent M82and the homozygous IL7-3 lines were also treated in the same way andmaintained as sterile plants in tissue culture. After 3-4 weeks themature leaves were harvested for the production of protoplasts.

Protoplast Isolation and Transfection

Isolation and regeneration of tomato leaf protoplasts has beenpreviously described (Shahin (1985) Theor.Appl.Genet. 69: 235-240; Tan(1987) Theor.Appl.Genet. 75: 105-108; Tan (1987) Plant Cell Rep. 6:172-175) and the solutions required can be found in these publications.Briefly, 1 g of freshly harvested leaves were placed in a dish with 5 mlCPW9M and, using a scalpel blade, cut perpendicular to the main stemevery mm. These were transferred a fresh plate of 25 ml enzyme solution(CPW9M containing 2% cellulose onozuka RS, 0.4% macerozyme onozuka R10,2.4-D (2 mg/ml), NAA (2 mg/ml), BAP (2 mg/ml) pH5.8) and digestionproceeded overnight at 25° C. in the dark. The protoplasts were thenfreed by placing them on an orbital shaker (40-50 rpm) for 1 hour.Protoplasts were separated from cellular debris by passing them througha 50 μm sieve, and washing the sieve 2× with CPW9M. Protoplasts werecentrifuged at 85 g, the supernatant discarded, and then taken up inhalf the volume of CPW9M. Protoplasts were finally taken up in 3 mlCPW9M and 3 ml CPW18S was then added carefully to avoid mixing the twosolutions. The protoplasts were spun at 85 g for 10 minutes and theviable protoplasts floating at the interphase layer were collected usinga long Pasteur pipette. The protoplast volume was increased to 10 ml byadding CPW9M and the number of recovered protoplasts was determined in ahaemocytometer. For transfection with a plasmid construct, theprotoplast suspension is centrifuged at 85×g for 10 minutes at 5° C. Thesupernatant is discarded and the protoplast pellet resuspended to afinal concentration of 106.mL-1 in KCl wash medium. In a 10 mL tube, 250μL of protoplast suspension +/−40 μg of pure plasmid DNA and 250 μl ofPEG solution (40% PEG4000 (Fluka #81240), 0.1M Ca(NO3)2, 0.4M mannitol)are gently but thoroughly mixed. After 20 min. incubation at roomtemperature, 5 mL cold 0.275 M Ca(NO3)2 is added drop wise. Theprotoplast suspension is centrifuged for 10 min at 85×g at 4° C. and thesupernatant discarded. After PEG treatment tomato protoplasts wereembedded in alginate solution for regeneration. 2 ml of alginatesolution was added (mannitol 90 g/l, CaCl2.2H2O 140 mg/l, alginate-Na 20g/l (Sigma A0602)) and was mixed thoroughly by inversion. 1 ml of thiswas layered evenly on a Ca-agar plate (72.5 g/l mannitol, 7.35 g/lCaCl2.2H2O, 8 g/l agar) and allowed to polymerize. The alginate discswere then transferred to 4 cm Petri dishes containing 4 ml of K8pculture medium and incubated in the dark at 30° C. for 7 days. Thealginate discs were then cut into 5 mm thick strips and layered on solidregeneration medium TM-DB (TM2 basal 2.5 g/l (Duchefa), Nitsch vitamins110 mg/l, sucrose 50 g/l, micro agar 8 g/l, 2,4-D 0.2 mg/l, BAP 0.5mg/l, pH5.8) for 3 weeks. Regenerated calli were then picked withtweezers and placed individually on GM-ZG medium (MS macro+micro powder(Duchefa) 4.3 g/l, Nitsch vitamins 110mg/I, mannitol 36.4 g/l, sucrose2.5 g/l, micro agar 8 g/l, zeatin 1 mg/l, GA3 1 mg/l, pH5.8). These werethen sampled for DNA isolation when they had reached approximately 7 mm.Upon shoot regeneration the calli were transferred to MS-ZI medium(MS+vitamins (Duchefa) 4.4 g/l, sucrose 20 g/l, micro agar 8 g/l, zeatin2 mg/l, IAA 0.1 mg/l, pH5.8). After 2-3 weeks shoots were excised andtransferred to rooting medium (MS+vitamins (Duchefa) 4.4 g/l, sucrose 20g/l, micro agar 8 g/l, 0.5 mg/ml IBA, pH5.8) and subsequently to thegreenhouse.

Sequencing of the S. pennellii ALS2 Locus

Chromosomal DNA was isolated from the homozygous IL7-3 line (DNeasy kit,Qiagen) and the Genome Walker kit (Clontech) was used to determine thesequence of the S. pennellii ALS2 locus as per the manufacturer'sinstructions. Briefly, 500 ng of genomic DNA was digested overnight witha restriction enzyme (Dral, EcoRV, Pvull or Stul), and the Genome Walkeradaptors were ligated. The ALS2 specific nested primers 11_11533(5′-TGGGAATGGTGGTTCAGTGGGAGGA-3′) and 11_11534(5′-GGTGGTTCAGTGGGAGGATCGATTCT-3′), designed on a conserved sequence inthe S. lycopersicum ALS2 ORF, were used to amplify the 3′ end of the S.pennellii ALS2 locus. Correspondingly, the nested primer pair 11_11536(5′-CGTAGCTCCCGGACCAGATGTAGCA-3′) and 11_11537(5′-ATGTAGCAATACAAACACCAGGGAACCCA-3′) were used to amplify the 5′ end ofthe ALS locus. The PCR products were excised from the gel and sequenced.Based on these sequences, additional primers (11_13680(TCACCCCTTCACCTTACC) and 11_13681 (CCTTCACATTTAACCAAAGC)) were designedthat amplified the intervening region and used to complete thesequencing of the locus (FIG. 2). In this way it was demonstrated thatthe ZFN target site in ALS2 was conserved in both the M82 and the IL7-3lines.

Design of ALS2 Locus Specific Primers

Alignment of the S. pennellii and M82 ALS2 sequence enabled us toidentify sequence differences which could be exploited for the design ofspecific primers which would selectively amplify only one of the allelesand which would amplify a PCR product that includes the ZFN target site.To amplify the S. pennellii ALS2 locus we used the primers11_13680+11_13681 and for the M82 ALS2 locus the primers 09Q136(GAAAGGGAAGGGGTTAAGG) and 12_07231 (CTTCAGTAGAGCCCTTGC) were used. Theresults are shown in FIG. 2a and show that these primers amplified aband of the correct size in the parental lines IL7-3 and M82 and thatboth loci were present in the F1 line derived from a cross of these twoparents (line BC).

Induction of INDELs at the S. pennellii ALS2 Locus

Protoplasts were isolated from both the IL7-3 line and M82 plants andtransfected either with plasmid pKG7402 or with a plasmid carrying a35S::GFP cassette (pKG7381). After 12 hours the protoplasts transfectedpKG7381 were observed under the fluorescent microscope to assess GFPexpression. This was equivalent in both the IL7-3 and the M82protoplasts (data not shown), demonstrating that the S. pennelliiintrogression in line IL7-3 did not affect transformation. After 48hours the protoplasts were harvested by centrifugation and genomic DNAwas isolated using the DNeasy kit (Qiagen). A PCR reaction was thenperformed on this DNA using primers 09Q132 (CTTGTGGAGGCACTTGAA) and09Q133 (CCGGACCAGATGTAGCAATA) which amplify a 205 bps fragment of theALS2 locus that includes the ZFN target site. The PCR product was thenpurified and cloned into a vector (pCR2.1:Blunt, Invitrogen) andtransformed to One Shot Chemically Competent E. coli cells (Invitrogen)as per the manufacturer's instructions and plated on LB mediumsupplemented with 50 μg/ml kanamycin (Duchefa). A PCR was subsequentlyperformed on individual 96 bacterial colonies using the same primers andthe resulting PCR products were analysed by High Resolution Meltingcurve analysis on a Roche Light Cycler apparatus to identify PCRproducts with aberrant melting characteristics. Such clones were thentaken for sequencing and the results are shown in FIG. 3. For both theIL7-3 and M82 lines, approximately 10% of the PCR products derived fromthe population of transfected protoplasts contained an INDEL at the ZFNtarget site. The size of these INDELs in both lines was also comparableand thus we can conclude that the S. pennellii ALS2 locus can betargeted as efficiently as the M82 ALS2 locus. As a control we alsoanalysed 96 PCR products derived from the pKG7381 transfection. None ofthese showed aberrant melting characteristics and when two weresequenced they did not show any alterations to the sequence (data notshown).

Targeted Translocations at the ALS2 Locus in Tomato Protoplasts

Protoplasts were isolated from in vitro grown F1 plants (derived from aM82×IL7-3 cross). In addition, we also isolated protoplasts from invitro grown M82 and IL7-3 plants. The protoplasts were transfected with40 μg of plasmid pKG7402 (or 40 μg of pKG7381 as a control) andmaintained in liquid medium for 48 hours. The protoplasts from eachtransfection were then harvested by centrifugation (800 rpm, 10 minutes)and genomic DNA was then isolated from these protoplast populationsusing the DNeasy kit (Qiagen). To detect the presence of translocationsin the protoplast population, combinations of the locus specific primerswere used. For instance, the combination of the S. pennellii ALS2 primer(11_13680) and the M82 primer (12_07231) should only amplify chromosomeswhich have undergone a translocation and will produce a PCR product thatincludes the translocation junction at the position of the ZFN targetsite. A PCR reaction using these primers was performed on all theprotoplast DNA samples using the following cycling conditions {95° C.2′; [95° C. 30″, 60° C. 30″, 72° C. 2′]×40; 72° C. 5′} in a reactionconsisting of 1 μl genomic protoplast DNA, 5 μl 5× Herculase Fusionbuffer (Agilent), 0.3 μl 100 mM dNTPs, 1.25 μl primer 11_13680, 1.25 μlprimer 12_07231, 0.25 μl Herculase II Fusion enzyme (Agilent) & 15.95 μlwater. Electrophoresis of the PCR products on a 1% agarose gel showedthat all samples produced a band of the expected size but that theintensity of the band was stronger in the F1 plant samples treated withpK7402 (data not shown). As we observed a PCR product in the controlsamples, this suggested that the primer combination 11_13680+12_07231was able to generate an aspecific PCR product from the unaltered S.pennellii and M82 ALS2 loci, but that the PCR product from the treatedF1 protoplasts may be stronger as in addition it contains PCR productsgenerated from translocation junctions. The 2.2 kbps PCR products fromboth the treatments and the controls were excised from the gel andpurified using the Qiagen Gel isolation kit. The PCR products were thencloned using the Zero Blunt PCR ligation kit (Invitrogen) following themanufacturer's instructions and the resulting plasmids containing thecloned products were purified from E. coli TOP10 cells and the complete2.2 kbps PCR products were sequenced. The results are shown in FIG. 4.The primers were indeed able to amplify an ALS2 PCR product from thecontrol samples but sequencing showed that these always were derivedfrom either the WT ALS2 locus (M82) or from the SpALS2 locus (IL7-3).Analysis of two PCR products derived from the F1 protoplasts transfectedwith the control plasmid (pKG7381) showed that both loci had beenamplified in this PCR reaction. All PCR products from the controlsshowed the expected sequence. The PCR products derived from the F1hybrid protoplasts treated with pKG7402 all showed a small INDEL at theZFN binding site, similar to those that we had earlier observed whenprotoplasts from the parental lines were treated with pKG7402. However,for each of these 2.2 kbps PCR products the SNP's upstream of the ZFNbinding site indicated that this was S. pennellii ALS2 sequence whilethe SNP's downstream of the ZFN binding site were derived from the M82ALS2 sequence, as we would expect for a translocation junction fragment.Therefore, this provided good evidence that in the population ofprotoplasts cells were present that had undergone a targetedtranslocation at the ALS2 locus between the S. pennellii introgressionand the WT M82 chromosome VII resulting in an exchange of chromosomearms and breaking of linkage in the introgression fragment.

To quantify how many protoplasts in the treated population contained atargeted translocation, we attempted to quantify the number of PCRproducts which have this characteristic S. pennellii/M82 ALS2 chimericorganization. We performed a PCR on the genomic DNA using the primers12_11216 (CTTCCACCCTTCTTCCCAAATC) and 12_11217 (TGCCAACTCCTGCACATTCA).These primers are not specific and so amplify a 1.3 kbps product fromboth the WT ALS2 and the SpALS2 loci. Such a PCR reaction thus consistsof SpALS2, WT ALS2, and targeted translocation products. To determinethe relative amounts of each these products in the PCR reaction, andthus the efficiency of the targeted translocation process itself, theproducts from the PCR reaction were cloned and genotyped. The 1.3 kbpsPCR product includes the ZFN binding site and two diagnostic restrictionsites located either side. Upstream of the ZFN binding site, an A→Gchange in the S. pennellii ALS2 sequence creates a HindIII restrictionsite. Downstream of the ZFN binding site a C→A change in the S.pennellii ALS2 sequence creates a Msel site. These sites were used as abasis for a CAPS assay to genotype PCR products for the ALS2 sequenceflanking the ZFN binding site. The 1.3 kbps PCR product was cloned usingthe Zero Blunt PCR Ligation kit as per the manufacturer's instructions.Individual bacterial colonies were then resuspended in 50 μl water,heated at 95° C. for 5 minutes and then 1 μl of this was used in anested PCR with the primers 09Q132+09Q133 or with 09R037+09R040 whichwere subsequently digested with HindIII or Msel respectively. Thepresence or absence of both the HindIII and the Msel sites wasindicative of an unaltered ALS2 locus (either SpALS2 or WT ALS2) whereasa cloned PCR product having only one of these PCR products may have beenderived from a targeted translocation event. In total 249 bacterialcolonies were genotyped for the presence of only one of theserestriction sites and five were eventually identified. For confirmation,the 1.3 kbps PCR products of these five clones were sequenced. Of thefive PCR products, we found two that had the expected organization (FIG.4). The first, clone #1, showed the S. pennellii ALS2 sequence upstreamof the ZFN binding site and the M82 ALS2 sequence downstream. For clone#2 this was reversed. Therefore, we can conclude that the efficiency oftargeted translocation formation in our experimental setup isapproximately 2 in 249 (0.8%). This suggests that only a limited numberof protoplasts need to be screened to isolate cells with targetedtranslocations.

Isolation of Tomato Plants with Targeted Translocations

Protoplasts were isolated from leaves of the F1 hybrid line andtransfected with 40 μg of plasmid pKG7402. For further development theywere then embedded in alginate discs which were then incubated in 4m1K8p medium for 7 days. The discs were then sliced into 5 mm strips whichwere then placed on solid TM-DB medium (2-4D, BAP) for furtherdevelopment of the microcalli. After 3 weeks growth 800 calli werepicked with forceps and transferred to fresh TM-DB medium. We have shownthat the translocation junctions always contain a small INDEL at the ZFNcut site and so we first screened all of the calli for this. Forgenotyping, a small piece of tissue was scraped from each developingcallus using a plastic pipette tip and then resuspended in 20 μl ofdilution buffer from the Phire Plant Direct PCR Kit (Thermo Scientific).For direct PCR on this material 1 μl of the dilution was taken and mixedwith 10 μl 2× reaction buffer, 2 μl of the primers 12_11216 and 12_11217(5 pmol) 0.2 μl of the Phire polymerase and water to a final reactionvolume of 20 μl. The PCR conditions used were; 98° C. 5 mins, {98° C. 5secs, 62° C. 5 secs, 72° C. 1.5 minutes} ×40, 72° C. 5 mins. These PCRproducts were then diluted 200× in water and 1 μl of this was used in anested PCR to amplify the ZFN cut site (1 μl PCR product, 5 μl 10×reaction buffer, 0.5 μl dNTPs (20 mM), 1 μl 09Q132 (5 pmol), 1 μl 09Q133(5 pmol), 0.2μl AmpliTaq (5U/μl) and 41.3 μl water with the cyclingconditions 94° C. 2 mins, {94° C. 30 secs, 55° C. 30 secs, 72° C. 30secs} ×30, 72° C. 5 mins. This generates a 200 bps PCR fragmentsincluding the ZFN cut site that can be screened for the presence ofINDELs. These PCR reactions were also carried out on material from theF1 line to generate control PCR products. To detect calli with INDELs atthe ZFN cut site, 4 μl of each 200 bps PCR product was mixed with 4 μlof the control PCR product and 1 μl of both TE and LC Green. The meltingcharacteristics of this mixture were then determined using the GeneScanning protocol of the Roche Light Cycler. We identified 53 sampleswith aberrant melting characteristics indicative of an INDEL at the ZFNcut site. The 1.3 kbps products from these 53 calli were then clonedusing the Zero Blunt PCR cloning kit (Invitrogen). Subsequently 4bacterial colonies from each ligation were genotyped for the presence ofthe HindIII and Msel sites as described above. From a single callus, TT1and TT2, we were able to show that all of the bacterial clones testedlacked one of the restriction sites, demonstrating that this cell hadundergone a reciprocal targeted translocation. These clones weresequenced and we were able to show that, similar to the sequencesderived from the protoplasts, a targeted translocation had occurred inthese calli. The frequency at which these calli were identified (0.25%)is in the same range as previously determined and remains unexpectedlyhigh.

Marker Analysis of RFPL's Flanking the S. pennellii Introgression

The calli TT1 and TT2 can then be transferred to shooting medium and thesubsequent shoots induced to form roots. The plants are then transferredto the greenhouse for further genotyping. Seed is collected from theplant TT1 and germinated in soil. Leaf material is harvested fromseedlings and DNA isolated. To demonstrate that the markers TG20 andTG143 are no longer linked in the progeny the seedlings are analyzed forthe presence of these markers. Selfing of the F1 plants, where the twomarkers are present on the same chromosome flanking the introgression,would be expected to give progeny where 25% lack either of the markersand 75% are positive for both markers. In a plant containing a targetedtranslocation the linkage between the markers has already been broken inthe protoplasts. When the progeny of such plants are analysed we wouldexpect 50% to have both markers (in this case located on differentchromosomes), 25% to contain only marker TG20 and 25% contain onlymarker TG143. Marker segregation analysis can be performed on theprogeny of the TT1 and TT2 plants. Therefore, the transient expressionof a site specific nuclease such as a ZFN in tomato protoplasts caninduce reciprocal targeted translocations that give viable plants andcan be transmitted to the next generation. This approach can be used tobreak any form of linkage between two DNA sequences in a sequenceindependent manner.

Example 2 Breaking the Linkage Drag at the TYLCV Locus

Tomato yellow curl leaf virus (TYLCV) is a devastating tomato diseasecaused by a begamovirus and transmitted by whitefly. TYLCV infection iscommon in warm (sub)tropical regions and this limits tomato growth inthese regions. Resistance to TYLCV infection has been found in severalwild tomato species (Ji et al. (2007) in Tomato Yellow Leaf Curl VirusDisease (Czosnek, H., ed). Netherlands: Springer, pp. 343-362).Currently, five resistance loci are used in breeding, Ty1 to Ty5. TheTy1 locus from S. chilense LA1969 was the first resistance locus to bemapped and is linked to the Ty3 locus on chromosome 6 and has beenincorporated into several commercially available varieties. However, theTy1 resistance locus suffers from linkage drag as it is accompanied byundesirable traits such as autonecrosis. The Ty1 locus is located in thepericentromeric region of chromosome 6 and is located on a 17 MBintrogression fragment which suffers from severe suppression ofrecombination. Verlaan et al. (2011, Plant J 68: 1096-1103) studiedrecombination at the Ty1 locus in 3000 F2 plants but were unable todetect any recombination events in their population over the majority ofthe introgression fragment. This appeared to be due to severalchromosomal rearrangements in S. chilense LA1969 which inhibitrecombination in this region during meiosis. As the production oftargeted translocations is homology independent, this can be used todecrease the size of the Ty1 locus in order to break the linkage dragand simplify the fine mapping of the Ty1 locus.

Several BAC's from S. lycopersicum have been identified that are presentin the Ty1 introgression fragment (Verlaan et al., 2011, Plant J 68:1096-1103). We used the sequence of one of these (H208D24, availablefrom: http://solgenomics.net/maps/physical/clone_info.pl?id=77280) toidentify genes that are likely to represent single copy sequences in thetomato genome. This BAC carries the tomato homolog of the A. thalianagene PRH75 (Plant RNA Helicase 75, At5g62190) annotated as Unigene SGNU268902. While this BAC was chosen arbitrarily, any other sequence inthe introgression region that is present on both chromosomes could alsobe used to perform these experiments. To identify nucleotide differencesat this locus between S. lycopersicum and S. chilense LA1969 GenomeWalking can be performed on this locus in both plant species. Thisallows the design PCR primers specific for the two SGN U268902 loci.Subsequently a TALEN construct can be designed that binds and cutsbetween the primer sites to validate its activity.

A plant line heterozygous for the Ty1 introgression is then cultivatedin vitro and protoplasts are isolated and transfected with the TALENplasmid DNA. Tomato protoplasts are then regenerated to callus andscreened using combinations of the SGN U268902 locus specific primers toidentify calli containing translocation junctions. These are thenregenerated to plants and selfed and the segregation of markers flankingthe SGN U268902 locus are determined. It is then possible to demonstratethat the size of the Ty1 introgression fragment had been reduced andthese plants can be analysed further for loss of linkage drag and for anassessment of the recombination frequencies at the shortenedintrogression fragments.

Example 3 Creating an Introdression of a Defined Size in Tomato BreedingMaterial and Fine Mapping of a Gene Responsible for Early Fruit Ripening

A tomato line, ER43, carrying a locus on chromosome I responsible forearly fruit ripening can be identified. Through marker analysis it canbe established that the locus is located between the AFLP markers MM101and MM107, which are separated by 527 kbps. The complete sequence ofthis region is available and so a series of target sequences can beselected spaced by 100 kbps which, based on BLAST analysis, are singlecopy sequences in the tomato genome. Primers are designed flanking thesetarget sequences and used to amplify the corresponding loci in thetomato line Moneymaker (available from:http://www.seedaholic.com/tomato-cherry-fox-organic-seeds-1.html) tofirstly confirm that the target sequences are identical in both linesand secondly to identify sequence differences around these targetsequences in the two tomato lines which can be exploited for the designof specific primers. Subsequently, five TALEN constructs are designed toproduce DSBs at these target sequences. The TALEN sequences are thensynthesized and cloned into a plasmid construct fusing the TALEN with apromoter sequence that is active in tomato protoplasts, such as thetomato AA6 promoter. Protoplasts of the ER43 and Moneymaker lines aretransfected with each TALEN plasmid, incubated for 24 hours in asuitable liquid medium, and then harvested by centrifugation. Thegenomic DNA is then isolated from each population of transfectedprotoplasts and each of the five target sequences is then amplifiedusing chromosome specific primers. The PCR products are then analysedfor the presence of INDELs at the target sequence, which would bepresent in around 10% of each batch of treated protoplasts. This willdemonstrate that the TALEN constructs are active in the cell and areable to induce DSBs at the target sequences of both tomato lines. LinesER43 and Moneymaker are then crossed to produce an F1 line which ismaintained under sterile conditions in tissue culture and used for theproduction of protoplasts.

These protoplasts are then transfected with the TALEN constructs and1000 calli derived from each transfection are grown and then genotypedfor the presence of a translocation at the target sequence usingdifferent combinations of the chromosome specific PCR primers. The callicontaining these targeted translocations are then regenerated intoplants and then selfed to create F2 plants that are homozygous for eachtranslocation. These are then phenotyped to identify the chromosomefragment carrying the early ripening locus. A physical map is thenconstructed of this region and the gene responsible for the earlyripening phenotype can be identified.

Example 4

Tarcieted Translocations in Brassica napus

Oliseed rape, or canola (Brassica napus) is an amphidiploid speciesformed from the interspecific hybridization of Brassica rapa (the Agenome) and Brassica oleraceae (the C genome). Selective pedigreebreeding has been intensively used to improve both yield and seedquality in this crop. Pedigree breeding involves the selection andinbreeding of superior F2 and later-generation individuals resultingfrom crosses between pairs of established cultivars. However, due to thelimited number of F2 plants screened the end products of the breedingprocess often contain large amounts of the parental genomes that give anegative effect on agronomic traits. This has been demonstrated in theB. napus type “Tapidor” that even after multiple generations ofbackcrossing still contained 29% of one of the parental genomes (Sharpe& Lydiate, 2001, Genome 46: 461-468). It is possible to calculate theprobability that a hypothetical F2 individual, derived from a F1carrying distinct donor and elite alleles in all genomic units, does notcontain any fixed donor genotype. This has been estimated to occurapproximately once in 81825 F2 plants (Sedcole, T. R. (1977) Crop Sci.17: 667-668). In contrast, pedigree breeding programs in oilseed rapegenerally only select from between 1000 and 2000 F2 plants, resulting inthe selection of an individual containing a large amount of unlinkeddonor genotype. Combined with the practice of producing doubled haploidsto increase the breeding speed, parental genotypes can become veryquickly homozygous and fixed, even when not linked to the locus ofinterest.

Due to the amphidiploid nature of B. napus, meiotic recombinationbetween the A and C genomes is prevented during meiosis. This is alsothe case for other amphidiploids species such as tobacco (Nicotianatabacum), durum wheat (Triticum durum), common wheat (Triticum aestivum)and cotton (Gossypium hirsutum). Considering an example in B. napus,agronomically important traits from parental lines can be introducedinto commercial lines through a breeding program which results in theparental locus, usually in a homozygous state, being present on one ofthe genomes (e.g. on the A genome). However, due to the restrictions onrecombination between the genomes during meiosis, the correspondinglocus on the C genome is unchanged. If this region also happens to carrysome negative phenotypes, or decreases the effectiveness of thephenotype conferred by the parental locus on the A genome, then thiscannot be easily resolved through conventional breeding. By inducing atargeted translocation between the A and C genomes using site directednucleases it is possible to produce a plant which is homozygous for theparental locus on both the A and C genomes (Schematically shown in FIG.5). Another possible application of this technology in polyploids is thetransfer of mutagen induced mutations between genomes to create fullyhomozygous lines. Mutation breeding is a common method of plantimprovement. It involves the treatment of plants, usually seed, with amutagen such as ethyl-methanosulfate (EMS) that generates C to T changesthroughout the genome. Mutated populations of plants are then grown,selfed, and in the following generation (M2) the plants are screened foraltered phenotypes (forward screen) or selected on the basis of inducedmutations in the gene of interest when the sequence is known (reversescreen). In many cases a mutation is required that confers a (complete)loss-of-function phenotype and this requires the identification of twoplant lines, each carrying a null mutation in the gene of interest inone of the genomes. These plants can then be crossed, the F1 selfed, andF2 plants identified which are homozygous for both null mutations onboth genomes. This is a very time consuming and expensive approach andbecomes harder with species such as hexaploid wheat when dealing withthree genomes. To avoid having to isolate independent mutations in eachgenome and then performing crosses we disclose that targetedtranslocations can be induced to transfer an induced (null) mutationbetween genomes and quickly reach a homozygous state (FIG. 5).

The experiments are focused on inducing a targeted translocation betweenthe B. napus chromosome 8 A and C genomes. The B. napus line “Tapidor”is selected for these experiments as it carries a large introgressionfragment on chromosome 8 of the A genome from the B. napus line“Bronowski” which contains many sequence differences with thecorresponding region on chromosome 8 of the C genome. A unique genepresent in both the A and C genomes is then identified and sequenced inthe “Tapidor” line to identify sequence differences. Based on these,primers are designed which only amplify the A or C genome locus. Toinduce a DNA DSB at both the loci on the A and C genomes, a TALENconstruct is designed. The A and C loci are screened for a sequenceidentical to both and TALENs are designed to bind and cut at thissequence. The TALEN's are cloned into a plasmid vector with aconstitutive plant promoter (35S) and are introduced into B. napus“Tapidor” protoplasts using PEG transfection. After 48 hours, DNA isisolated from the protoplasts and the locus specific primers are used togenerate PCR products which are sequenced to demonstrate that the TALENconstruct is able to induce INDEL's at the target site. The experimentis then repeated and individual B. napus calli are regenerated andgenotyped for the presence of targeted translocations by usingcombinations of the A and C genome locus specific primers. Individualcalli can be identified that have targeted translocations at theexpected positions and also different sized INDELs in chromosome 8 (e.g.4 bps in the A genome, 3 bps in the C genome) representing differentINDELs at the translocation junctions in the hybrid A and C chromosomes.Plants are then regenerated from these calli and grown to maturity. Thenext generation is then screened for seedlings that are homozygous forthese INDELs and these are also homozygous for the remainder of thechromosome arm.

Example 5 Fusion of Locus Domains Using Targeted Translocations

The plant line IR3 has a strong resistance to a wide range of insectsdue to the presence of an insecticidal compound at high concentration inits trichomes. This high concentration is achieved by a high expressionof one of genes (IK4) involved in the biochemical synthesis of thiscompound. The high expression is achieved by a novel promoter whichdrives high transcriptional activation in a trichome specific manner.The plant line IR12 also contains the IK4 gene, but is susceptible toinsect feeding. Molecular analysis has shown that the IK4 gene is notexpressed in the trichomes of IR12 and that this is due to nucleotidedifferences in the promoter of the IK4 gene in the IR12 line which leadsto its inactivation. The goal of these experiments was to restore thehigh trichome specific expression of the IK4 gene in the IR12 line byinducing a targeted translocation between the lines, resulting in thefusion of the IR3 promoter with the IK4 gene from line IR12. A targetsequence is identified located 20 bps upstream of the IK4 ORF and aTALEN is designed to create a DSB at this site. The TALEN is then clonedbehind a suitable promoter for plant expression and the resultingplasmid is then transfected to protoplasts from both the IR3 and IR12lines. As described in example 3, in this way we are able to confirmthat the TALEN expression is able to induce a DSB at the target sequencein both plant lines. A F1 line is then made by crossing the IR3 and IR12lines and is then used to produce protoplasts that are then transfectedwith the TALEN construct. As described in other examples, specificprimers amplifying either the IR3 or the IR12 locus are used indifferent combinations to identify calli in which a targetedtranslocation has occurred. These calli are then regenerated into plantsand then backcrossed to the IR12 parent plant several times, selectingfor the targeted translocation in each generation, to reach a situationwhere the plant is isogenic to the IR12 parent except for the desiredtranslocation. Using quantitative RT-PCR it can be shown that that inthis line the precise fusion of the IR3 promoter to the IR4 IK4 gene hasrestored high IK4 expression in the trichomes and subsequent phenotypingdemonstrates that this plant shows strong resistance to a wide range ofinsects. This example demonstrates that translocations can be used tofuse promoter or other regulatory sequences to genes of another line andthus achieve novel expression patterns giving valuable phenotypes.

Example 6 Creating Novel Open Reading Frames Using TargetedTranslocations

Resistance to fungal pathogens is often conferred by the class ofleucine rich repeat (LRR) genes located in resistance gene clustersdistributed throughout the plant genome. Plant line M17 contains a LRRresistance gene (LRR12) conferring specific resistance to the race 1 ofthe fungal pathogen that causes the disease late blight. The plant lineP15 carries a similar resistance gene cluster located at the sameposition on the chromosome. In P15, the resistance gene most similar insequence to LRR12, named LRR63, is located at the same position in thecluster but has a different amino acid sequence. As a consequence theLRR63 gene confers resistance to fungal race 2 but not the race 1.Neither of these resistance genes confers resistance to the fungal race3. Our hypothesis is that novel resistance to fungal race 3 can beachieved by combining domains of the LRR12 and LRR63 genes. The sequenceof both of these genes is known and the introns are analysed forsequences that were present in both LRR12 and LRR63. A site specificnuclease is then designed that is able to induce a DSB at this targetsequence. The site specific nuclease is then cloned behind a promoterproviding expression in plant protoplasts and the resulting plasmid isthen used to transfect protoplasts from both the plant lines M17 andP15. As described in more detail in the other examples included herein,we are able to demonstrate that the site specific nuclease is able toproduce DSBs at the intron target sequences in both LRR12 and LRR63. AF1 line is then produced by crossing the M17 and P15 lines and ismaintained in sterile conditions in tissue culture. Protoplasts are thenisolated from the F1 line and transfected with the plasmid encoding thesite specific nuclease. Individual protoplasts are then regenerated tocalli and these are genotyped with combinations of specific primersdesigned for LRR12 or LRR63 to detect calli in which a targetedtranslocation has occurred. As the translocation has been targeted in anintron, the small INDELs that are produced during the translocation onlyremove part of the intron sequence and therefore do not affect the geneopen reading frame. The translocation results in the fusion of domainsof the LRR12 gene with domains of the LRR63 gene, creating a novel geneconferring new resistances. The calli with the translocation areregenerated into plants and it can be demonstrated that the new chimericopen reading frame is made up of domains from both LRR12 and LRR63 andthat it provides novel resistance to fungal race 3. This exampledemonstrates how targeted translocations can be used to join domainsfrom different genes together to create novel genes conferring importantnew phenotypes.

Example 7 Simultaneous Induction of Targeted Translocations andInhibition of Meiosis

Targeted translocations can be induced between homoeologous chromosomesin a F1 hybrid using site specific nucleases. The individual calli canthen be regenerated to produce plants that then proceed through normalmeiosis leading to a normal F2 population with genomic segments fromboth parental plants. Extensive backcrossing is then required to obtainisogenic lines for phenotyping which can take years and involvesmultiple rounds of population screening. An isogenic line can beobtained in a single generation when meiotic crossovers are inhibited inthe original plant allowing the parental chromosomes to segregaterandomly in the gametes. Most gametes will be non-viable due to abnormalchromosome number, but a small percentage will contain all thechromosomes of the desired parent and when used in a direct backcrosswith the required parent will generate an isogenic line in a singlegeneration. The targeted translocation to be produced can be any ofthose described in examples 1 to 6. Protoplasts can be produced from F1plants and simultaneously transfected with two plasmids. The firstplasmid carries a site specific nuclease, driven by a promoter active inplant protoplasts, that produces the desired targeted translocation asalready described. The second plasmid carries a different site specificnuclease, driven by a second promoter active in plant protoplasts thatis designed to create a DSB in a gene, Dmc1, involved in crossoverformation during meiosis. Repair of this DSB will produce small INDELsin the meiotic gene leading to a complete loss of gene function. Calliare then selected containing the desired targeted translocation andthese are then screened for additional homozygous INDEL mutations at thetarget sequence of Dmc1. These calli are then regenerated to plants andbackcrossed to the original parent plant. It can be demonstrated thatthe plants derived from this cross contain the desired translocation butotherwise are isogenic with the backcross parent. Thus, this method canbe applied to generate lines containing targeted translocations andwhich are otherwise also isogenic to one of the parental lines withoutthe need for an extensive backcrossing program.

1. A method for inducing a targeted translocation between a first locusA and a second locus B present on a first plant chromosome in a plant orplant cell, the method comprising: (a) providing at least one plant cellcomprising: (i) the first chromosome comprising an introgressioncomprising the first locus A and the second locus B, wherein the firstlocus A and the second locus B exhibit linkage drag with one another;and (ii) at least a second chromosome, wherein the chromosomes arehomologous or homeologous chromosomes of each other; (b) introducing adouble strand break at a target sequence in the first chromosome,wherein the double strand break in the first chromosome is introducedbetween the first locus A and the second locus B thereby providing afirst part of the first chromosome comprising the first locus A and asecond part of the first chromosome comprising the second locus B; (c)introducing a double strand break in the second chromosome, therebyproviding a first part of the second chromosome and a second part of thesecond chromosome; and (d) identifying, using the at least one plantcell obtained under (c), at least one plant cell comprising atranslocation between the first locus A and the second locus B on thefirst chromosome, and wherein the first part of the first chromosomecomprising the first locus A is ligated to the second part of the secondchromosome by non-homologous end joining, wherein the double strandbreak in the first chromosome and the double strand break in the secondchromosome is introduced by at least one site-specific nuclease selectedfrom the group consisting of a zinc finger nuclease, a meganuclease, aTAL-effector nuclease or a nuclease of CRISPR system introduced into theat least one plant cell of (a).
 2. The method of claim 1, wherein themethod is for: (i) breaking linkage drag; (ii) tailored introgressions;(iii) fine mapping; (iv) intra-genic recombination; (v) generation ofgene fusions; and (vi) targeted manipulation of allopolyploid, diploid,triploid, tetraploid, pentaploid, hexaploid, octaploid, decaploid,dodecaploid or an amphidiploid plant genome.
 3. The method of claim 2,wherein the method is for intra-genic recombination and/or generation ofgene fusions.
 4. The method of claim 1, wherein in (d), the second partof the first chromosome is ligated to the first part of the secondchromosome.
 5. The method of claim 1, wherein the second chromosome doesnot comprise a locus that is identical to the first locus A and/or doesnot comprise a locus that is identical to the second locus B.
 6. Themethod according to claim 1, wherein multiple site-specific nucleasesare used for introducing the double strand break in the first chromosomeand/or the double strand break in the second chromosome.
 7. The methodof claim 1, wherein the double strand break in the first chromosome andthe double strand break in the second chromosome are introduced by thesame site-specific nuclease.
 8. The method according to claim 1, whereinlocus A and/or locus B are part of a gene.
 9. The method according toclaim 8, wherein locus A and/or locus B are part of a promoter.
 10. Themethod of claim 1, wherein no more than one double strand break isintroduced in the first chromosome and no more than one double strandbreak is introduced in the second chromosome.
 11. The method accordingto claim 1, wherein the identifying in (d) comprises any one ofsequencing, selective amplification of ligated parts of the firstchromosome, phenotyping the offspring and fluorescent in-situhybridisation (FISH).
 12. The method of claim 1, further comprising: (e)regenerating a plant from a plant cell obtained after step (c) of claim1; (f) generating seed from the regenerated plant by selfing or crossingwith another plant; (g) growing a plant from seed obtained in step (f),and; (h) optionally, screening the plant obtained in step (g) fortargeted translocation.
 13. The method of claim 1, wherein the providedplant cell is a somatic plant cell.
 14. The method of claim 13, whereinthe somatic plant cell is selected from the group consisting of aprotoplast, and/or a plant cell obtained from a hybrid.
 15. The methodof claim 1, wherein the plant is a diploid, triploid, tetraploid,pentaploid, hexaploid, octaploid, decaploid, dodecaploid or aamphidiploid.
 16. A method for providing a plant P1 obtained from aplant P2, wherein the plant P2 is characterized by the presence of afirst locus A and a second locus B on a first chromosome, wherein thefirst locus A and the second locus B exhibit linkage drag with oneanother, and wherein the plant P1 is characterized by the presence of atargeted translocation between the first locus A and the second locus B,the method comprising: (a) providing at least one plant cell from theplant P2 comprising the first chromosome comprising an introgressioncomprising the first locus A and the second locus B and furthercomprising at least a second chromosome, wherein the chromosomes arehomologous or homeologous chromosomes of each other; (b) introducing adouble strand break at a target sequence in the first chromosome,wherein the double strand break in the first chromosome is introducedbetween the first locus A and the second locus B, thereby providing afirst part of the first chromosome comprising the first locus A and asecond part of the first chromosome comprising the second locus B; (c)introducing a double strand break in the second chromosome, therebyproviding a first part of the second chromosome and a second part of thesecond chromosome; (d) identifying, using the at least one plant cellobtained under step (c), at least one plant cell comprising atranslocation between the first locus A and the second locus B on thefirst chromosome, and further, wherein the first part of the firstchromosome comprising the first locus A is ligated to the second part ofthe second chromosome by non-homologous end joining; and (e)regenerating the plant P1 from the at least one plant cell identified in(d); wherein the double strand break in the first chromosome and thedouble strand break in the second chromosome is introduced by at leastone site-specific nuclease selected from the group consisting of a zincfinger nuclease, a meganuclease, a TAL-effector nuclease or a nucleaseof CRISPR system introduced into the at least one plant cell of (a).